Similar to bacteria that have adapted to frequently used antibiotics over time, super weeds have gained immunity to herbicides. Weed scientists estimate there are more than 400 different herbicide-resistant weeds around the world. Resistant weeds hurt crops by competing for sunlight and nutrients.

St. Louis-based Monsanto’s biotechnology team has been working on two new soybean and cotton varieties designed to withstand dicamba – an infrequently used herbicide that weeds have not caught up with yet – for nearly a decade.

“These new technologies will help farmers achieve better harvests, which will help meet the demand to nourish the growing population,” said Miriam Paris, Monsanto’s Xtend system launch manager.

Propelled by recent U.S. Department of Agriculture deregulation, Monsanto anticipates the seeds will help fight the super weeds and lead what a January first-quarter earnings report labeled the largest biotechnology launch in company history.

The varieties were fully deregulated by the USDA’s Animal and Plant Health Inspection Service on Jan. 15. They will be part of the company’s Roundup Ready Xtend package and are scheduled for a 2016 launch. The USDA deregulation followed a profitable year for Monsanto, as the company’sannual report shows it posted $2.74 billion in net income for 2014.

While small-scale farmers and industry officials have welcomed the deregulation, critics worry it will prompt a greater dependence on the toxic chemicals that caused the super weed problem in the first place.

“I think APHIS is being entirely irresponsible in terms of its obligations to the public and to the environment,” said Doug Gurian-Sherman, senior scientist and director of the sustainable agriculture program for the Center for Food Safety, a national nonprofit advocacy group that supports organic and sustainable agriculture.

Currently, 1 percent of all soybean acres are treated with the 1960s’ herbicide dicamba.

If farmers planted the new Monsanto crops, USDA assessments warn dicamba use would increase by about 88-fold in soybeans and about 14-fold in cotton.

“In the medium to longer run, commercializing these crops without any real mandatory controls on how they’re used is going to lead to a lot of environmental and potentially human health problems,” said Gurian-Sherman, a plant pathologist by trade who has also worked for the Environmental Protection Agency. “They are going to just exacerbate what we’re already seeing.”

Although the company’s soybean and cotton varieties cleared one required hurdle by earning USDA approval, the varieties still cannot enter market until EPA approves their related use of dicamba. The USDA, the EPA and the Food and Drug Administration share the responsibility of commercializing all new genetically engineered crops.

The FDA has already supported deregulation.

The EPA will finalize its assessment later this year.

“U.S. soybean and cotton growers continue to tell us that they need these products to help manage tough-to-control weeds on their farms, and we remain committed to commercializing these next-generation technologies, pending regulatory approval,” Paris said.

Foreign countries will need to approve the cotton and soybean before Monsanto could export the varieties, as well.

Canada and Australia are among the countries that have approved the herbicide-resistant cotton.

Monsanto, founded in 1901, made a lasting impact in the agriculture industry during the 1990s with the introduction of its genetically engineered Roundup Ready crops created to resist glyphosate, the herbicide of choice for many farmers.

With the introduction, farmers were able to plant Roundup Ready seeds knowing they could safely use glyphosate to efficiently kill any weeds that popped up in their fields. The products saved farmers time and energy, while also allowing them to till their fields less frequently.

“I remember when Roundup Ready soybeans first came out,” said Jeff Bunting, crop protection division manager for the agriculture cooperative Growmark headquartered in Bloomington, Ill. “Glyphosate, being a broad spectrum herbicide, controlled many of the weeds that we had issues with and were dealing with.”

Herbicide-resistant soybeans were so effective that U.S. farmers planted varieties on nearly every acre. In 2011, roughly 90 percent of soybean acres were planted with genetically engineered seeds, according to USDA data.

The technology helped make the U.S. soybean and cotton industries the multi-billion dollar sectors they are today.

In 2013, U.S. farmers planted more than 10.4 million acres of cotton worth more than $5 billion. The same year, farmers planted more than 76.8 million acres of soybean worth slightly less than $42 billion.

But the weeds adapted.

“Too much of one thing is probably not good,” said Bunting, who grew up on a family farm in east central Illinois and has been pulling weeds from soybean fields since he could barely see over the plants.

As weeds adapted, Monsanto started to experiment with new technology with oversight from the Animal and Plant Health Inspection Service. In 2006, the company began testing dicamba-resistant soybean and cotton – which were also still resistant to glyphosate – in 19 states and Puerto Rico. Combined, the tests were distributed throughout more than 180,000 acres.

USDA agency balances deregulation and ‘protecting plants’

Monsanto routinely spends more than $1 billion annually on research and development. Its annual report shows the company spent more than $1.73 billion in 2014 and more than $1.53 billion the previous two years.

“Our crops and technologies undergo a rigorous and in-depth review by third-party scientists and government agencies and have a proven safety record with no adverse effects to people, wildlife or the environment,” Paris said.

Other companies have followed suit.

Each year, the Animal and Plant Health Inspection Service receives 10,000 to 11,000 requests for testing authorization, according to Michael Firko, the agency’s deputy administrator and head of its biotechnology regulatory team.

Since 2006, the agency – armed with inspectors in throughout the country – monitored Monsanto’s results and ensured the genetically engineered cotton and soybeans were not planted too close to already approved crops. During the testing period, the agency also issued permits to select farmers who sought to grow the soybean and cotton.

“We’re in the business of protecting plants,” Firko said.

Then, Monsanto submitted a request for deregulation in 2012.

“After a developer has been field testing a plant for a number of years,” Firko said. “They may come to us and say, ‘Ok, we’ve got something that we’ve been working on, and we don’t think it represents any plant pest risk.’”

Under the Plant Protection Act passed in 2000, the Animal and Plant Health Inspection Service evaluates whether a genetically engineered crop would pose a “plant pest” once deregulated. Another piece of legislation, the National Environmental Policy Act, requires the agency to publish its findings, typically in a smaller environmental assessment or a larger environmental impact statement.

In its review of Monsanto’s dicamba-resistant soybean and cotton seeds, the agency compiled an impact statement, which Firko said is the “most complete environmental analysis that can be done.”

The Animal and Plant Health Inspection Service published a draft statement in August. It published its final statement in December, which was then subject to a 30-day public viewing window before completion.

Both versions recommended “full deregulation,” concluding the Monsanto soybean and cotton would be “widely used” by growers.

“It is clear there is high demand in the market from farmers,” Paris said. “Farmers will ultimately determine the value based on on-farm use.

Critics question regulatory oversight

Gurian-Sherman said the regulatory process that shepherded the Monsanto soybean and cotton toward deregulation is “limited” and “in shambles.”

The main problem is a “loophole” in jurisdiction, he said.

The Animal and Plant Health Inspection Service determined in its impact statement that the deregulation of new genetically engineered crops would likely result in an increased development of weeds resistant to dicamba. The agency found that the soybean and cotton do not pose a direct plant pest risk alone, but their overuse would repeat the same problem that happened with glyphosate and the early Roundup Ready crops.

But since it is tasked with identifying direct plant pests and not indirect consequences, the agency settled on deregulation.

“The USDA, APHIS, has very limited authority to really regulate the risks from these crops,” Gurian-Sherman said.

Others were also critical. Between Monsanto’s initial filing and the Animal and Plant Health Inspection Service’s final environmental impact statement, the agency provided more than 180 days for the public to comment on the petition.

Individuals and groups posted more than 4,700 comments during that time.

“Increased use of genetically engineered crops such as dicamba cotton is not the answer to super weed problems – do not approve it,” commenter Roslyn Fedberg wrote.

“Please work to move farming away from an over-reliance on chemical agriculture,” another commenter, Tom Bellamy, wrote.

Gurian-Sherman said the petition received so many public comments because agriculture is connected to important topics that people care about, such as food safety and environmental stewardship.

“The way we do agriculture has huge impacts on people’s lives,” he said.